William Pearman
@williampearman.bsky.social
Research fellow at Auckland Uni. Wannabe bioinformatician, reluctant community ecologist. Evolutionary ecology, microbial ecology. Anglican. He/him
We thought about it, but the dna wasn't usually particularly high molecular weight nor was it viscous so we never tried shearing
September 4, 2025 at 7:07 PM
We thought about it, but the dna wasn't usually particularly high molecular weight nor was it viscous so we never tried shearing
Yeah absolutely - so in kelp DNA for example we did some LCMS and found the likely culprit for blockages was polyphenols bound to the DNA onlinelibrary.wiley.com/doi/full/10....
But in the case of some of this data, it was supposedly 'pure' DNA from the zymo mock community.
But in the case of some of this data, it was supposedly 'pure' DNA from the zymo mock community.
September 4, 2025 at 2:33 AM
Yeah absolutely - so in kelp DNA for example we did some LCMS and found the likely culprit for blockages was polyphenols bound to the DNA onlinelibrary.wiley.com/doi/full/10....
But in the case of some of this data, it was supposedly 'pure' DNA from the zymo mock community.
But in the case of some of this data, it was supposedly 'pure' DNA from the zymo mock community.
I did try to see if the signal or quality change before the blockage - funnily enough the quality tended to be higher at the end of the read when it terminated due to a block, than when it terminated due to completing the read. But really just haven't had motivation recently do the proper deep dive.
September 4, 2025 at 2:31 AM
I did try to see if the signal or quality change before the blockage - funnily enough the quality tended to be higher at the end of the read when it terminated due to a block, than when it terminated due to completing the read. But really just haven't had motivation recently do the proper deep dive.
Granted, this was from a quick and dirty analysis I did a year or so ago, but I tried it with the zymo mock community and also observed the same sort of thing. So i'm just curious as to whether the GC-rich sequences are more likely to block. Just for context, the 'combined' is all reads together.
September 4, 2025 at 2:24 AM
Granted, this was from a quick and dirty analysis I did a year or so ago, but I tried it with the zymo mock community and also observed the same sort of thing. So i'm just curious as to whether the GC-rich sequences are more likely to block. Just for context, the 'combined' is all reads together.
Curious as to your thoughts - if I look at metagenomic datasets from ONT sequencing, and separate them based on end reason (i.e., blocked pore vs completely navigated the poor) - I find two very different communities. The grouping is based on the terminal base of DNA sequence (misc metagenomic data)
September 4, 2025 at 2:21 AM
Curious as to your thoughts - if I look at metagenomic datasets from ONT sequencing, and separate them based on end reason (i.e., blocked pore vs completely navigated the poor) - I find two very different communities. The grouping is based on the terminal base of DNA sequence (misc metagenomic data)